KABUL (Reuters) - Twelve people were killed on Friday in the bloodiest day yet in protests that have raged across Afghanistan over the desecration of copies of the Muslim holy book at a NATO military base with riot police and soldiers on high alert braced for more violence.

The burning of the Korans at the Bagram compound earlier this week has deepened public mistrust of NATO forces struggling to stabilise Afghanistan before foreign combat troops withdraw in 2014.

Hundreds of Afghans marched towards the palace of Afghan President Hamid Karzai in Kabul, while on the other side of the capital protesters hoisted the white flag of the Taliban.

Chanting "Death to America!" and "Long live Islam!", protesters also threw rocks at police in Kabul, while Afghan army helicopters circled above.

Friday is a holy day and the official weekly holiday in Afghanistan and mosques in the capital drew large crowds, with police in pick-up trucks posted on nearby streets.

Armed protesters took refuge in shops in the eastern part of the city, where they killed one demonstrator, said police at the scene. In another Kabul rally, police said they were unsure who fired the shots that killed a second protester.

Seven more protesters were killed in the western province of Herat, two more in eastern Khost province and one in the relatively peaceful northern Baghlan province, health and local officials said. In Herat, around 500 men charged at the U.S. consulate.

U.S. President Barack Obama had sent a letter to Karzai apologising for the unintentional burning of the Korans at NATO's main Bagram air base, north of Kabul, after Afghan labourers found charred copies while collecting rubbish.

Muslims consider the Koran to be the literal word of God and treat each copy with deep reverence. Desecration is considered one of the worst forms of blasphemy.

Afghanistan wants NATO to put those responsible on public trial.

In neighbouring U.S. ally Pakistan, about 400 members of a hardline Islamist group staged protests. "If you burn the Koran, we will burn you," they shouted.

To Afghanistan's west, Iranian cleric Ahmad Khatami said the U.S. had purposely burned the Korans. "These apologies are fake. The world should know that America is against Islam," he said in a speech broadcast live on state radio.

"It (the Koran burning) was not a mistake. It was an intentional move, done on purpose."

Most Westerners have been confined to their heavily fortified compounds, including at the sprawling U.S. embassy complex and other diplomatic missions, as protests that have killed a total of 23 people, including two U.S. soldiers, rolled into their fourth day.

The embassy, in a message on the microblogging site Twitter, urged U.S. citizens to "please be safe out there" and expanded movement restrictions to relatively peaceful northern provinces, where large demonstrations also occurred on Thursday, including the attempted storming of a Norwegian military base.

The Taliban urged Afghan security forces on Thursday to "turn their guns on the foreign infidel invaders" and repeatedly urged Afghans to kill, beat and capture NATO soldiers.

Germany, which has the third-largest foreign presence in the NATO-led war, pulled out several weeks early of a small base in the northern Takhar province on Friday over security concerns, a defence ministry spokesman said.

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